Wombat coprogenetics: enumerating a common wombat population by microsatellite analysis of faecal DNA

Genetic identification of individual animals from remotely collected DNA samples provides an alternative approach for the collection of data on populations of elusive or rare species. In this study we used DNA isolated from field-collected faecal samples to estimate the size of a population of common wombats (Vombatus ursinus) surviving in suburban Melbourne parkland. A pilot study revealed that microsatellite genotypes obtained from DNA in faeces were often incorrect, but that by carrying out three replicate polymerase chain reactions (PCRs) for each sample, we were able to reliably identify individuals. We conducted a mark-recapture study using the Mh-jackknife model to estimate the size of the wombat population at Mt Lofty Reserve, and identified 17 individuals - 10 males and seven females. The interpolated population size estimate was 19 with a 95% confidence interval of 18-32. The distribution of individual wombats' scats provided information on ranging behaviour. The genotypic database obtained was used to identify five of the individuals as putative immigrants, suggesting that the population is not isolated from others in a series of reserves along the Yarra River. However, the lack of a detectable female bias in immigration differs from our previous findings in continuous populations of this species. The level of genetic variation at the five loci analysed was also inconsistent with long-term isolation of the population.

[1]  J. Mcilroy.  Aspects of the ecology of the common wombat, Vombatus ursinus (Shaw, 1800) , 1973 .

[2]  J. Mcilroy.  Aspects of the Ecology of the Common Wombat, Vombatus ursinus II. Methods for Estimating Population Numbers , 1977 .

[3]  K. Burnham,et al.  Estimation of the size of a closed population when capture probabilities vary among animals , 1978 .

[4]  David R. Anderson,et al.  Statistical inference from capture data on closed animal populations , 1980 .

[5]  François Rousset,et al.  GENEPOP (version 1.2): population genetic software for exact tests and ecumenicism , 1995 .

[6]  R. Deuter,et al.  A method for preparation of fecal DNA suitable for PCR. , 1995, Nucleic acids research.

[7]  J. Goudet.  FSTAT (Version 1.2): A Computer Program to Calculate F-Statistics , 1995 .

[8]  P. Taberlet,et al.  Owl pellets as a source of DNA for genetic studies of small mammals , 1996, Molecular ecology.

[9]  H. Whitehead,et al.  Patterns of kinship in groups of free-living sperm whales (Physeter macrocephalus) revealed by multiple molecular genetic analyses. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Ross Goldingay,et al.  The wombat : common wombats in Australia , 1996 .

[11]  P Taberlet,et al.  Reliable genotyping of samples with very low DNA quantities using PCR. , 1996, Nucleic acids research.

[12]  S. Wasser,et al.  Techniques for application of faecal DNA methods to field studies of Ursids , 1997, Molecular ecology.

[13]  L. Waits,et al.  Noninvasive genetic tracking of the endangered Pyrenean brown bear population , 1997, Molecular ecology.

[14]  Christopher N. Johnson,et al.  Relatedness structure detected by microsatellite analysis and attempted pedigree reconstruction in an endangered marsupial, the northern hairy‐nosed wombat Lasiorhinus krefftii , 1997, Molecular ecology.

[15]  C Boesch,et al.  Microsatellite scoring errors associated with noninvasive genotyping based on nuclear DNA amplified from shed hair , 1997, Molecular ecology.

[16]  R. Hudson,et al.  Genetic tagging of humpback whales , 1997, Nature.

[17]  B. Rannala,et al.  Detecting immigration by using multilocus genotypes. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[18]  B. Goossens,et al.  Plucked hair samples as a source of DNA: reliability of dinucleotide microsatellite genotyping , 1998, Molecular ecology.

[19]  R. Ward,et al.  Variation in Genetic Diversity across the Range of North American Brown Bears , 1998 .

[20]  L. Waits,et al.  Noninvasive genetic sampling: look before you leap. , 1999, Trends in ecology & evolution.

[21]  G Luikart,et al.  New methods employing multilocus genotypes to select or exclude populations as origins of individuals. , 1999, Genetics.

[22]  David Paetkau,et al.  Genetic tagging of free-ranging black and brown bears , 1999 .

[23]  Pierre Taberlet,et al.  Non-invasive genetic sampling and individual identification , 1999 .

[24]  R. Wayne,et al.  Estimating population size by genotyping faeces , 1999, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[25]  M. Beaumont.  Detecting population expansion and decline using microsatellites. , 1999, Genetics.

[26]  Flagstad,et al.  Reliable noninvasive genotyping based on excremental PCR of nuclear DNA purified with a magnetic bead protocol , 1999, Molecular ecology.

[27]  M. Syvanen,et al.  Molecular tracking of mountain lions in the Yosemite Valley region in California: genetic analysis using microsatellites and faecal DNA , 2000, Molecular ecology.

[28]  G. Mowat,et al.  Estimating population size of grizzly bears using hair capture, DNA profiling, and mark-recapture analysis , 2000 .

[29]  Paul L. Leberg,et al.  Biases associated with population estimation using molecular tagging , 2000 .

[30]  Michael K. Schwartz,et al.  ESTIMATING ANIMAL ABUNDANCE USING NONINVASIVE DNA SAMPLING: PROMISE AND PITFALLS , 2000 .

[31]  L. Waits,et al.  Estimating the probability of identity among genotypes in natural populations: cautions and guidelines , 2001, Molecular ecology.

[32]  Lounès Chikhi,et al.  A multi-samples, multi-extracts approach for microsatellite analysis of faecal samples in an arboreal ape , 2000, Conservation Genetics.

[33]  S. Banks,et al.  A set of microsatellite loci for the hairy-nosed wombats (Lasiorhinus krefftii and L. latifrons) , 2000, Conservation Genetics.